Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing

PLoS One. 2017 May 25;12(5):e0178425. doi: 10.1371/journal.pone.0178425. eCollection 2017.

Abstract

In this study, we designed a microcosm experiment to explore the composition of the bacterial community in the rhizosphere of maize and bulk soil by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina system. 978-1239 OTUs (cut off level of 3%) were found in rhizosphere and bulk soil samples. Rhizosphere shared features with the bulk soil, such as predominance of Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes and TM7. At genus level, many of the dominant rhizosphere genera (Chitinophaga, Nitrospira, Flavobacterium, etc.) displayed different patterns of temporal changes in the rhizosphere as opposed to the bulk soil, showing rhizosphere has more impact on soil microorganisms. Besides, we found that significant growth-related dynamic changes in bacterial community structure were mainly associated with phylum Bacteroidetes, Proteobacteria and Actinobacteria (mainly genera Burkholderia, Flavisolibacter and Pseudomonas), indicating that different growth stages affected the bacterial community composition in maize soil. Furthermore, some unique genera in especial Plant-Growth Promoting Rhizobacteria (PGPR) such as Nonomuraea, Thiobacillus and Bradyrhizobium etc., which were beneficial for the plant growth appeared to be more abundant in the rhizosphere than bulk soil, indicating that the selectivity of root to rhizosphere microbial is an important mechanism leading to the differences in the bacteria community structure between rhizosphere and bulk soil.

Publication types

  • Comparative Study

MeSH terms

  • Bacteria / genetics*
  • Plant Roots / microbiology*
  • RNA, Ribosomal, 16S / genetics
  • Rhizosphere
  • Sequence Analysis, DNA / methods
  • Soil
  • Soil Microbiology
  • Zea mays / microbiology*

Substances

  • RNA, Ribosomal, 16S
  • Soil

Grants and funding

This study was financially support by the Natural Science Foundation of China (No. 21507037), Commonwealth and Environmental Protection Project granted by the MEP (No. 201309031), as well as the Fundamental Research Funds for NIES in 2016 “Source Apportionment Research of antibiotics pollution in typical drinking water resource”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.